// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
//
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted (subject to the limitations in the
// disclaimer below) provided that the following conditions are met:
//
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//
//  * Redistributions in binary form must reproduce the above
//    copyright notice, this list of conditions and the following
//    disclaimer in the documentation and/or other materials provided
//    with the distribution.
//
//  * Neither the name of Pacific Biosciences nor the names of its
//    contributors may be used to endorse or promote products derived
//    from this software without specific prior written permission.
//
// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
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// SUCH DAMAGE.

// Author: Mark Chaisson

#ifndef _BLASR_ENUMERATIONS_HPP_
#define _BLASR_ENUMERATIONS_HPP_

typedef enum T_FileType {Fasta,
    Fastq,
    HDFPulse,
    Fourbit,
    HDFBase,
    HDFCCS,
    HDFCCSONLY,
    PBBAM,
    None
} FileType;

typedef enum T_Strand {Forward, Reverse} Strand;

typedef enum T_PlatformType {
    Springfield,
    Astro,
    NoPlatform
} PlatformId;

typedef enum T_RegionType {
    Adapter,
    Insert, 
    HQRegion,
    BarCode,
    UnknownRegionType
} RegionType;

typedef enum T_PulseMetricType {
    QualityValueMetric,ClassifierQVMetric,StartTimeMetric,PulseWidthMetric,WidthInFramesMetric,
    pkmidMetric,IPDMetric,LightMetric, PreBaseFramesMetric
} PulseMetricType;


typedef enum T_AlignMode { NoAlignMode, Fullread, Subread, CCSDeNovo, CCSFullPass, CCSAllPass, ZmwSubreads } AlignMode;

#endif
